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Sodium in PDB 6rij: CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436

Enzymatic activity of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436

All present enzymatic activity of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436:
2.7.11.22;

Protein crystallography data

The structure of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436, PDB code: 6rij was solved by J.Skerlova, P.Rezacova, J.Brynda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 162.95 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.310, 148.060, 162.960, 90.00, 90.51, 90.00
R / Rfree (%) 20.4 / 23.8

Sodium Binding Sites:

The binding sites of Sodium atom in the CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436 (pdb code 6rij). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436, PDB code: 6rij:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6rij

Go back to Sodium Binding Sites List in 6rij
Sodium binding site 1 out of 4 in the CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:38.5
occ:1.00
O A:HOH413 3.1 40.0 1.0
O A:HOH416 3.2 38.6 1.0
N A:TYR269 3.5 34.9 1.0
CG2 A:VAL226 3.7 79.8 1.0
CD2 A:HIS268 3.8 50.2 1.0
CD2 A:TYR269 3.9 38.1 1.0
NE2 A:HIS268 3.9 49.8 1.0
CG A:HIS268 3.9 46.5 1.0
CA A:HIS268 4.0 35.9 1.0
CB A:TYR269 4.0 38.5 1.0
CE1 A:HIS268 4.0 53.5 1.0
ND1 A:HIS268 4.1 52.7 1.0
C A:HIS268 4.2 34.0 1.0
NH1 A:ARG245 4.4 43.5 1.0
CA A:TYR269 4.4 35.7 1.0
CG A:TYR269 4.4 38.5 1.0
CG1 A:VAL226 4.5 63.3 1.0
CB A:HIS268 4.6 42.8 1.0
CB A:VAL226 4.8 64.7 1.0
CE2 A:TYR269 4.9 37.2 1.0
O A:LEU267 5.0 33.3 1.0

Sodium binding site 2 out of 4 in 6rij

Go back to Sodium Binding Sites List in 6rij
Sodium binding site 2 out of 4 in the CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:50.2
occ:1.00
O B:GLN203 2.5 51.4 1.0
O B:MET200 2.6 54.4 1.0
O B:ILE206 2.7 44.8 1.0
C B:GLN203 3.7 51.1 1.0
C B:MET200 3.7 57.5 1.0
C B:ILE206 3.8 45.0 1.0
CB B:GLN203 4.3 54.7 1.0
O B:LYS201 4.3 61.2 1.0
CA B:GLN203 4.3 54.0 1.0
CG B:MET200 4.4 55.9 1.0
N B:GLN203 4.4 52.9 1.0
N B:LYS201 4.5 58.8 1.0
CA B:THR207 4.5 48.4 1.0
C B:LYS201 4.5 61.4 1.0
CG2 B:THR207 4.6 49.2 1.0
CA B:LYS201 4.6 64.2 1.0
N B:ILE206 4.6 47.6 1.0
N B:THR207 4.6 47.7 1.0
CA B:MET200 4.7 54.2 1.0
N B:PRO204 4.8 52.2 1.0
C B:PRO204 4.8 57.8 1.0
CA B:ILE206 4.8 46.9 1.0
O B:PRO204 4.9 61.3 1.0
SD B:MET200 4.9 58.3 1.0

Sodium binding site 3 out of 4 in 6rij

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Sodium binding site 3 out of 4 in the CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:39.2
occ:1.00
O C:HOH420 3.0 37.1 1.0
O C:HOH408 3.3 35.4 1.0
N C:TYR269 3.4 34.4 1.0
CD2 C:HIS268 3.7 51.0 1.0
NE2 C:HIS268 3.8 54.8 1.0
CG2 C:VAL226 3.9 79.6 1.0
CD2 C:TYR269 3.9 35.1 1.0
CG C:HIS268 3.9 48.4 1.0
CA C:HIS268 4.0 37.7 1.0
CE1 C:HIS268 4.1 55.5 1.0
CB C:TYR269 4.1 34.7 1.0
ND1 C:HIS268 4.1 53.5 1.0
C C:HIS268 4.2 36.6 1.0
CA C:TYR269 4.4 34.8 1.0
CG C:TYR269 4.4 35.3 1.0
NH1 C:ARG245 4.5 43.1 1.0
CB C:HIS268 4.6 41.8 1.0
CG1 C:VAL226 4.7 67.1 1.0
O C:LEU267 4.9 35.4 1.0
CE2 C:TYR269 4.9 32.6 1.0
CB C:VAL226 4.9 69.0 1.0

Sodium binding site 4 out of 4 in 6rij

Go back to Sodium Binding Sites List in 6rij
Sodium binding site 4 out of 4 in the CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:46.4
occ:1.00
O D:GLN203 2.6 50.3 1.0
O D:MET200 2.6 60.2 1.0
O D:ILE206 2.7 42.4 1.0
C D:MET200 3.7 58.9 1.0
C D:GLN203 3.8 52.9 1.0
C D:ILE206 3.9 45.1 1.0
O D:LYS201 4.3 59.4 1.0
CB D:GLN203 4.3 54.9 1.0
CG D:MET200 4.4 53.1 1.0
CA D:GLN203 4.4 52.7 1.0
CG2 D:THR207 4.4 47.8 1.0
N D:GLN203 4.4 54.4 1.0
N D:LYS201 4.4 65.4 1.0
C D:LYS201 4.5 65.0 1.0
CA D:LYS201 4.5 69.3 1.0
CA D:THR207 4.5 46.3 1.0
O D:HOH637 4.5 43.5 1.0
N D:THR207 4.7 44.3 1.0
O D:PRO204 4.7 57.6 1.0
CA D:MET200 4.7 55.4 1.0
N D:ILE206 4.7 45.5 1.0
C D:PRO204 4.8 55.3 1.0
N D:PRO204 4.8 49.6 1.0
SD D:MET200 4.9 54.9 1.0
CB D:MET200 5.0 52.1 1.0
CA D:ILE206 5.0 47.5 1.0

Reference:

J.Skerlova, P.Rezacova, J.Brynda. CDK2/Cyclin A2 in Complex with Open-Ring 5-Nitrosopyrimidine Inhibitor LC436 To Be Published.
Page generated: Tue Dec 15 12:54:27 2020

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